Equipped with the core genome sequence, the team collected still more sequence data from ten male flycatchers of each species, and aligned these additional sequences to the genome sequence, identifying millions of sites that vary within the two species, and millions of sites where they share variants. They scanned through all these sites to identify points in the genome where differences between the two small samples of flycatchers were completely fixed — that is, sites where all the collared flycatcher sequences carried one variant, and all the pied flycatcher sequences carried a different variant. The frequency of these fixed differences varied considerably across the genome, but there are dozens of spots where they’re especially concentrated, forming peaks of differentiation.

To learn what all those “islands of divergence” could tell us about how the two flycatchers came to be different species, go read the whole thing.◼